1 Input parameters

Table 1.1: Input parameters.

1.1 Log files loaded

  • SRR1383451_add-meta_command_log.txt
  • SRR1383451_changeo_assigngenes_command_log.txt
  • SRR1383451_collapse_command_log.txt
  • SRR1383451_fq_command_log.txt
  • SRR1383451_jmod3_command_log.txt
  • SRR1383451_makedb_command_log.txt
  • SRR1383451_split_command_log.txt
  • SRR1383452_add-meta_command_log.txt
  • SRR1383452_changeo_assigngenes_command_log.txt
  • SRR1383452_collapse_command_log.txt
  • SRR1383452_fq_command_log.txt
  • SRR1383452_jmod3_command_log.txt
  • SRR1383452_makedb_command_log.txt
  • SRR1383452_split_command_log.txt
  • SRR1383453_add-meta_command_log.txt
  • SRR1383453_changeo_assigngenes_command_log.txt
  • SRR1383453_collapse_command_log.txt
  • SRR1383453_fq_command_log.txt
  • SRR1383453_jmod3_command_log.txt
  • SRR1383453_makedb_command_log.txt
  • SRR1383453_split_command_log.txt
  • SRR1383456_add-meta_command_log.txt
  • SRR1383456_changeo_assigngenes_command_log.txt
  • SRR1383456_collapse_command_log.txt
  • SRR1383456_fq_command_log.txt
  • SRR1383456_jmod3_command_log.txt
  • SRR1383456_makedb_command_log.txt
  • SRR1383456_split_command_log.txt
  • SRR1383463_add-meta_command_log.txt
  • SRR1383463_changeo_assigngenes_command_log.txt
  • SRR1383463_collapse_command_log.txt
  • SRR1383463_fq_command_log.txt
  • SRR1383463_jmod3_command_log.txt
  • SRR1383463_makedb_command_log.txt
  • SRR1383463_split_command_log.txt
  • SRR1383464_add-meta_command_log.txt
  • SRR1383464_changeo_assigngenes_command_log.txt
  • SRR1383464_collapse_command_log.txt
  • SRR1383464_fq_command_log.txt
  • SRR1383464_jmod3_command_log.txt
  • SRR1383464_makedb_command_log.txt
  • SRR1383464_split_command_log.txt
  • SRR1383465_add-meta_command_log.txt
  • SRR1383465_changeo_assigngenes_command_log.txt
  • SRR1383465_collapse_command_log.txt
  • SRR1383465_fq_command_log.txt
  • SRR1383465_jmod3_command_log.txt
  • SRR1383465_makedb_command_log.txt
  • SRR1383465_split_command_log.txt
  • SRR1383466_add-meta_command_log.txt
  • SRR1383466_changeo_assigngenes_command_log.txt
  • SRR1383466_collapse_command_log.txt
  • SRR1383466_fq_command_log.txt
  • SRR1383466_jmod3_command_log.txt
  • SRR1383466_makedb_command_log.txt
  • SRR1383466_split_command_log.txt
  • SRR1383467_add-meta_command_log.txt
  • SRR1383467_changeo_assigngenes_command_log.txt
  • SRR1383467_collapse_command_log.txt
  • SRR1383467_fq_command_log.txt
  • SRR1383467_jmod3_command_log.txt
  • SRR1383467_makedb_command_log.txt
  • SRR1383467_split_command_log.txt
  • SRR1383468_add-meta_command_log.txt
  • SRR1383468_changeo_assigngenes_command_log.txt
  • SRR1383468_collapse_command_log.txt
  • SRR1383468_fq_command_log.txt
  • SRR1383468_jmod3_command_log.txt
  • SRR1383468_makedb_command_log.txt
  • SRR1383468_split_command_log.txt

2 Workflow

3 File processing

3.1 SRR1383452_db-pass.tsv

3.1.1 Data flow

Number of sequences at each processing step of SRR1383452_db-pass.tsv.

3.1.2 Barplot

Number of reads at different stages of the processing of SRR1383452_db-pass.tsv File can be found here: SRR1383452_db-pass.tsv ggplot file: SRR1383452_db-pass.RData

3.2 SRR1383464_db-pass.tsv

3.2.1 Data flow

Number of sequences at each processing step of SRR1383464_db-pass.tsv.

3.2.2 Barplot

Number of reads at different stages of the processing of SRR1383464_db-pass.tsv File can be found here: SRR1383464_db-pass.tsv ggplot file: SRR1383464_db-pass.RData

3.3 SRR1383451_quality-pass.tsv

3.3.1 Data flow

Number of sequences at each processing step of SRR1383451_quality-pass.tsv.

3.3.2 Barplot

Number of reads at different stages of the processing of SRR1383451_quality-pass.tsv File can be found here: SRR1383451_quality-pass.tsv ggplot file: SRR1383451_quality-pass.RData

3.4 SRR1383467_meta-pass.tsv

3.4.1 Data flow

Number of sequences at each processing step of SRR1383467_meta-pass.tsv.

3.4.2 Barplot

Number of reads at different stages of the processing of SRR1383467_meta-pass.tsv File can be found here: SRR1383467_meta-pass.tsv ggplot file: SRR1383467_meta-pass.RData

3.5 SRR1383453_igblast.fmt7

3.5.1 Data flow

Number of sequences at each processing step of SRR1383453_igblast.fmt7.

3.5.2 Barplot

Number of reads at different stages of the processing of SRR1383453_igblast.fmt7 File can be found here: SRR1383453_igblast.tsv ggplot file: SRR1383453_igblast.RData

3.6 SRR1383456_junction-pass.tsv

3.6.1 Data flow

Number of sequences at each processing step of SRR1383456_junction-pass.tsv.

3.6.2 Barplot

Number of reads at different stages of the processing of SRR1383456_junction-pass.tsv File can be found here: SRR1383456_junction-pass.tsv ggplot file: SRR1383456_junction-pass.RData

3.7 SRR1383466_meta-pass.tsv

3.7.1 Data flow

Number of sequences at each processing step of SRR1383466_meta-pass.tsv.

3.7.2 Barplot

Number of reads at different stages of the processing of SRR1383466_meta-pass.tsv File can be found here: SRR1383466_meta-pass.tsv ggplot file: SRR1383466_meta-pass.RData

3.8 SRR1383468_db-pass.tsv

3.8.1 Data flow

Number of sequences at each processing step of SRR1383468_db-pass.tsv.

3.8.2 Barplot

Number of reads at different stages of the processing of SRR1383468_db-pass.tsv File can be found here: SRR1383468_db-pass.tsv ggplot file: SRR1383468_db-pass.RData

3.9 SRR1383465_igblast.fmt7

3.9.1 Data flow

Number of sequences at each processing step of SRR1383465_igblast.fmt7.

3.9.2 Barplot

Number of reads at different stages of the processing of SRR1383465_igblast.fmt7 File can be found here: SRR1383465_igblast.tsv ggplot file: SRR1383465_igblast.RData

3.10 SRR1383463_meta-pass.tsv

3.10.1 Data flow

Number of sequences at each processing step of SRR1383463_meta-pass.tsv.

3.10.2 Barplot

Number of reads at different stages of the processing of SRR1383463_meta-pass.tsv File can be found here: SRR1383463_meta-pass.tsv ggplot file: SRR1383463_meta-pass.RData

4 Final table

Figure 4.1: Number of sequences at each processing step. ggplot file: sequence_count_plot.RData

Table 4.1: Table showing the number of sequences at each processing step. file_0 is the first file for each sample analysis tree. File can be found here: log_data.tsv

5 Software versions

## R version 4.4.2 (2024-10-31)
## Platform: x86_64-redhat-linux-gnu
## Running under: Fedora Linux 40 (Container Image)
## 
## Matrix products: default
## BLAS/LAPACK: FlexiBLAS OPENBLAS-OPENMP;  LAPACK version 3.11.0
## 
## locale:
## [1] C
## 
## time zone: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] plotly_4.10.4   ggplot2_3.5.1   tidyr_1.3.1     dplyr_1.1.4    
## [5] enchantr_0.1.19
## 
## loaded via a namespace (and not attached):
##   [1] bitops_1.0-9                airr_1.5.0                 
##   [3] gridExtra_2.3               rlang_1.1.4                
##   [5] magrittr_2.0.3              clue_0.3-66                
##   [7] GetoptLong_1.0.5            ade4_1.7-22                
##   [9] matrixStats_1.4.1           compiler_4.4.2             
##  [11] png_0.1-8                   vctrs_0.6.5                
##  [13] stringr_1.5.1               pkgconfig_2.0.3            
##  [15] shape_1.4.6.1               crayon_1.5.3               
##  [17] fastmap_1.2.0               XVector_0.46.0             
##  [19] labeling_0.4.3              ggraph_2.2.1               
##  [21] utf8_1.2.4                  Rsamtools_2.22.0           
##  [23] rmarkdown_2.29              tzdb_0.4.0                 
##  [25] UCSC.utils_1.2.0            purrr_1.0.2                
##  [27] xfun_0.49                   zlibbioc_1.52.0            
##  [29] cachem_1.1.0                seqinr_4.2-36              
##  [31] GenomeInfoDb_1.42.0         jsonlite_1.8.9             
##  [33] progress_1.2.3              DelayedArray_0.32.0        
##  [35] BiocParallel_1.40.0         tweenr_2.0.3               
##  [37] parallel_4.4.2              prettyunits_1.2.0          
##  [39] cluster_2.1.6               R6_2.5.1                   
##  [41] bslib_0.8.0                 stringi_1.8.4              
##  [43] RColorBrewer_1.1-3          jquerylib_0.1.4            
##  [45] GenomicRanges_1.58.0        bookdown_0.41              
##  [47] knitr_1.49                  Rcpp_1.0.13-1              
##  [49] SummarizedExperiment_1.36.0 iterators_1.0.14           
##  [51] readr_2.1.5                 IRanges_2.40.0             
##  [53] Matrix_1.7-1                igraph_2.1.1               
##  [55] tidyselect_1.2.1            rstudioapi_0.17.1          
##  [57] abind_1.4-8                 yaml_2.3.10                
##  [59] viridis_0.6.5               doParallel_1.0.17          
##  [61] codetools_0.2-20            lattice_0.22-6             
##  [63] tibble_3.2.1                Biobase_2.66.0             
##  [65] withr_3.0.2                 evaluate_1.0.1             
##  [67] polyclip_1.10-7             circlize_0.4.16            
##  [69] Biostrings_2.74.0           pillar_1.9.0               
##  [71] MatrixGenerics_1.18.0       DT_0.33                    
##  [73] foreach_1.5.2               stats4_4.4.2               
##  [75] generics_0.1.3              S4Vectors_0.44.0           
##  [77] hms_1.1.3                   munsell_0.5.1              
##  [79] scales_1.3.0                glue_1.8.0                 
##  [81] lazyeval_0.2.2              tools_4.4.2                
##  [83] data.table_1.16.2           GenomicAlignments_1.42.0   
##  [85] graphlayouts_1.2.1          tidygraph_1.3.1            
##  [87] grid_4.4.2                  ape_5.8                    
##  [89] crosstalk_1.2.1             colorspace_2.1-1           
##  [91] nlme_3.1-166                GenomeInfoDbData_1.2.13    
##  [93] ggforce_0.4.2               cli_3.6.3                  
##  [95] alakazam_1.3.0              fansi_1.0.6                
##  [97] S4Arrays_1.6.0              viridisLite_0.4.2          
##  [99] ComplexHeatmap_2.18.0       gtable_0.3.6               
## [101] sass_0.4.9                  digest_0.6.37              
## [103] BiocGenerics_0.52.0         SparseArray_1.6.0          
## [105] ggrepel_0.9.6               rjson_0.2.23               
## [107] htmlwidgets_1.6.4           farver_2.1.2               
## [109] memoise_2.0.1               htmltools_0.5.8.1          
## [111] lifecycle_1.0.4             httr_1.4.7                 
## [113] GlobalOptions_0.1.2         MASS_7.3-61